Useful R functions (detailed)

← Flow control (if/else, for) Self-study assignment →

Sandbox vectors

Let’s define some vectors which can be used for demonstrations:

manyNumbers <- sample( 1:1000, 20 )
manyNumbers

 [1] 633 174 212 623 176 527 845 241 462 570 342 644  83 205 969 676 985  50 512 726

manyNumbersWithNA <- sample( c( NA, NA, NA, manyNumbers ) )
manyNumbersWithNA

 [1] 462 241  83 985 676 176 633 205 512 726 644 174 623  NA 527  NA 969 845 342  NA 570  50 212

duplicatedNumbers <- sample( 1:5, 10, replace = TRUE )
duplicatedNumbers

 [1] 5 3 1 1 5 4 2 2 5 1

letters

 [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "y" "z"

LETTERS

 [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T" "U" "V" "W" "X" "Y" "Z"

mixedLetters <- c( sample( letters, 5 ), sample( LETTERS, 5 ) )
mixedLetters

 [1] "m" "y" "z" "q" "w" "J" "F" "K" "L" "P"

Are all/any elements TRUE

• Input: logical vector
• Output: single logical value
• Task: try, understand what happens when you use manyNumbersWithNA instead of manyNumbers.

all( manyNumbers <= 1000 )

[1] TRUE

all( manyNumbers <= 500 )

[1] FALSE

any( manyNumbers > 1000 )

[1] FALSE

any( manyNumbers > 500 )

[1] TRUE

all( !is.na( manyNumbers ) )

[1] TRUE

any( is.na( manyNumbers ) )

[1] FALSE

Which elements are TRUE

Input: logical vector Output: vector of numbers (positions)

which( manyNumbers > 900 )

[1] 15 17

which( manyNumbersWithNA > 900 )

[1]  4 17

which( is.na( manyNumbersWithNA ) )

[1] 14 16 20

Filtering vector elements

• Input: any vector and filtering condition
• Output: elements of the input vector
• Note: several ways to get the same effect

manyNumbers[ manyNumbers > 900 ] # indexing by logical vector

[1] 969 985

manyNumbers[ which( manyNumbers > 900 ) ] # indexing by positions

[1] 969 985

somePositions <- which( manyNumbers > 900 )
manyNumbers[ somePositions ]

[1] 969 985

Are some elements among other elements

• Input: two vectors
• Output: a logical vector corresponding to the first input vector

"A" %in% LETTERS

[1] TRUE

c( "X", "Y", "Z" ) %in% LETTERS

[1] TRUE TRUE TRUE

all( c( "X", "Y", "Z" ) %in% LETTERS )

[1] TRUE

all( mixedLetters %in% LETTERS )

[1] FALSE

any( mixedLetters %in% LETTERS )

[1] TRUE

mixedLetters[ mixedLetters %in% LETTERS ]

[1] "J" "F" "K" "L" "P"

mixedLetters[ !( mixedLetters %in% LETTERS ) ]

[1] "m" "y" "z" "q" "w"

manyNumbers %in% 300:600

 [1] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
[18] FALSE  TRUE FALSE

which( manyNumbers %in% 300:600 )

[1]  6  9 10 11 19

sum( manyNumbers %in% 300:600 )

[1] 5

Pick one of two (three) depending on condition

• Input: a logical vector and two vectors additional vectors (for TRUE, for FALSE)
• Output: elements of the additional vectors
• Note: it can take care of NAs

if_else( manyNumbersWithNA >= 500, "large", "small" )

 [1] "small" "small" "small" "large" "large" "small" "large" "small" "large" "large" "large" "small" "large"
[14] NA      "large" NA      "large" "large" "small" NA      "large" "small" "small"

if_else( manyNumbersWithNA >= 500, "large", "small", "UNKNOWN" )

 [1] "small"   "small"   "small"   "large"   "large"   "small"   "large"   "small"   "large"   "large"  
[11] "large"   "small"   "large"   "UNKNOWN" "large"   "UNKNOWN" "large"   "large"   "small"   "UNKNOWN"
[21] "large"   "small"   "small"  

# here integer 0L is needed instead of real 0.0 
# manyNumbersWithNA contains integer numbers and the method complains
if_else( manyNumbersWithNA >= 500, manyNumbersWithNA, 0L ) 

 [1]   0   0   0 985 676   0 633   0 512 726 644   0 623  NA 527  NA 969 845   0  NA 570   0   0

Duplicates and unique elements

• Input: a vector

unique( duplicatedNumbers )

[1] 5 3 1 4 2

unique( c( NA, duplicatedNumbers, NA ) )

[1] NA  5  3  1  4  2

duplicated( duplicatedNumbers )

 [1] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE

Positions of max/min elements

which.max( manyNumbersWithNA )

[1] 4

manyNumbersWithNA[ which.max( manyNumbersWithNA ) ]

[1] 985

which.min( manyNumbersWithNA )

[1] 22

manyNumbersWithNA[ which.min( manyNumbersWithNA ) ]

[1] 50

range( manyNumbersWithNA, na.rm = TRUE )

[1]  50 985

Sorting/ordering of vectors

manyNumbersWithNA

 [1] 462 241  83 985 676 176 633 205 512 726 644 174 623  NA 527  NA 969 845 342  NA 570  50 212

sort( manyNumbersWithNA )

 [1]  50  83 174 176 205 212 241 342 462 512 527 570 623 633 644 676 726 845 969 985

sort( manyNumbersWithNA, na.last = TRUE )

 [1]  50  83 174 176 205 212 241 342 462 512 527 570 623 633 644 676 726 845 969 985  NA  NA  NA

sort( manyNumbersWithNA, na.last = TRUE, decreasing = TRUE )

 [1] 985 969 845 726 676 644 633 623 570 527 512 462 342 241 212 205 176 174  83  50  NA  NA  NA

manyNumbersWithNA[1:5]

[1] 462 241  83 985 676

order( manyNumbersWithNA[1:5] )

[1] 3 2 1 5 4

rank( manyNumbersWithNA[1:5] )

[1] 3 2 1 5 4

sort( mixedLetters )

 [1] "F" "J" "K" "L" "m" "P" "q" "w" "y" "z"

Ranking of vectors

manyDuplicates <- sample( 10:15, 10, replace = TRUE )
rank( manyDuplicates )

 [1] 2.0 5.0 7.5 5.0 9.5 5.0 2.0 9.5 2.0 7.5

rank( manyDuplicates, ties.method = "min" )

 [1] 1 4 7 4 9 4 1 9 1 7

rank( manyDuplicates, ties.method = "random" )

 [1]  1  6  8  5  9  4  2 10  3  7

Rounding numbers

v <- c( -1, -0.5, 0, 0.5, 1, rnorm( 10 ) )
v

 [1] -1.00000000 -0.50000000  0.00000000  0.50000000  1.00000000 -0.55700252  0.28980461  0.02789515
 [9]  0.27340777  0.43334730 -0.28217503 -0.30836190 -0.48783588 -0.86480465  0.88774686

round( v, 0 )

 [1] -1  0  0  0  1 -1  0  0  0  0  0  0  0 -1  1

round( v, 1 )

 [1] -1.0 -0.5  0.0  0.5  1.0 -0.6  0.3  0.0  0.3  0.4 -0.3 -0.3 -0.5 -0.9  0.9

round( v, 2 )

 [1] -1.00 -0.50  0.00  0.50  1.00 -0.56  0.29  0.03  0.27  0.43 -0.28 -0.31 -0.49 -0.86  0.89

floor( v )

 [1] -1 -1  0  0  1 -1  0  0  0  0 -1 -1 -1 -1  0

ceiling( v )

 [1] -1  0  0  1  1  0  1  1  1  1  0  0  0  0  1

Naming vector elements

heights <- c( Amy = 166, Eve = 170, Bob = 177 )
heights

Amy Eve Bob 
166 170 177 

names( heights )

[1] "Amy" "Eve" "Bob"

names( heights ) <- c( "AMY", "EVE", "BOB" )
heights

AMY EVE BOB 
166 170 177 

heights[[ "EVE" ]]

[1] 170

Generating grids

expand_grid( x = c( 1:3, NA ), y = c( "a", "b" ) )

# A tibble: 8 x 2
      x y    
  <int> <chr>
1     1 a    
2     1 b    
3     2 a    
4     2 b    
5     3 a    
6     3 b    
7    NA a    
8    NA b    

Generating combinations

combn( c( "a", "b", "c", "d", "e" ), m = 2, simplify = TRUE )

     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] "a"  "a"  "a"  "a"  "b"  "b"  "b"  "c"  "c"  "d"  
[2,] "b"  "c"  "d"  "e"  "c"  "d"  "e"  "d"  "e"  "e"  

combn( c( "a", "b", "c", "d", "e" ), m = 3, simplify = TRUE )

     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] "a"  "a"  "a"  "a"  "a"  "a"  "b"  "b"  "b"  "c"  
[2,] "b"  "b"  "b"  "c"  "c"  "d"  "c"  "c"  "d"  "d"  
[3,] "c"  "d"  "e"  "d"  "e"  "e"  "d"  "e"  "e"  "e"  

← Flow control (if/else, for) Self-study assignment →

---

Copyright © 2021 Biomedical Data Sciences (BDS) | LUMC